Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Mokrishcheva, Marina L ^a,b   Solonin, Alexander S ^a   Nikitin, Dmitri V ^a  

^a SKRYABIN INSTITUTE OF BIOCHEMISTRY AND PHYSIOLOGY OF MICROORGANISMS   (Russian Federation)

^b PUSHCHINO STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DIVERGENCE; ENZYME ACTIVITY; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; GENETIC ENGINEERING; PEPTIDE; POLYMER;

BACTERIAL PROTEIN; CCGCGG SPECIFIC TYPE II DEOXYRIBONUCLEASES; CCGCGG-SPECIFIC TYPE II DEOXYRIBONUCLEASES; DNA METHYLTRANSFERASE; HYBRID PROTEIN; PEPTIDE; RESTRICTION ENDONUCLEASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; EVOLUTION; GENETICS; METABOLISM; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOLOGICAL EVOLUTION; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA MODIFICATION METHYLASES; DNA RESTRICTION-MODIFICATION ENZYMES; MOLECULAR SEQUENCE DATA; PEPTIDES; RECOMBINANT FUSION PROTEINS; SEQUENCE ALIGNMENT;

EID: 79551565616     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-35     Document Type: Article

References (35)

1. Restriction endonucleases: classification, properties, and applications. RJ Williams, Mol Biotechnol (Pubitemid 36308437)
2. KJ Skowronek JM Bujnicki, Industrial Enzymes: Structure, Function and Applications Springer, Polaina J, MacCabe AP, 2007 Chapter 21
3. REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. RJ Roberts T Vincze J Posfai D Macelis, Nucl Acids Res 2010 38 234 236 10.1093/nar/gkp874
4. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. RJ Roberts M Belfort T Bestor AS Bhagwat TA Bickle J Bitinaite RM Blumenthal S Degtyarev DT Dryden K Dybvig, et al. Nucleic Acids Res 2003 31 1805 1812 10.1093/nar/gkg274 12654995 (Pubitemid 36437486)
5. Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli. A Pertzev N Ruban M Zakharova I Beletzkaja S Petrov A Kravetz A Solonin, Nucleic Acids Res 1992 20 1991 10.1093/nar/20.8.1991 1579502
6. Complete nucleotide sequence of the Hsd plasmid pECO29 and identification of its functional regions. M Zakharova A Pertzev A Kravetz I Beletskaya M Shlyapnikov A Solonin, Bioch Bioph Acta 1998 1398 106 112 (Pubitemid 28305205)
7. Cloning and sequence analysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes. M Zakharova I Beletskaya A Kravetz A Pertzev S Mayorov M Shlyapnikov A Solonin, Gene 1998 208 177 182 10.1016/S0378-1119(97)00637-9 9524260 (Pubitemid 28120927)
8. Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. J Bujnicki M Radlinska L Rychlewski, TREND in Biochemical Sciences 2001 26 9 11 10.1016/S0968-0004(00) 01690-X (Pubitemid 32124698)
9. Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. E Ibryashkina M Zakharova V Baskunov E Bogdanova M Nagornykh M Den'mukhamedov B Melnik A Kolinski D Gront M Feder A Solonin J Bujnicki, BMC Struct Biol 2007 7 48 10.1186/1472-6807-7-48 17626614
10. Oligomeric structure diversity within the GIY-YIG nuclease family. M Ibryashkina G Sasnauskas A Solonin M Zakharova V Siksnys, J Mol Biol 2009 387 10 16 10.1016/j.jmb.2009.01.048 19361436
11. Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression. A Karyagina I Shilov V Tashlitskii M Khodoun S Vasil'ev P Lau I Nikolskaya, Nucleic Acids Res 1997 25 2114 2120 10.1093/nar/25.11.2114 9153310 (Pubitemid 27303446)
12. Organization of restriction-modification systems. GG Wilson, Nucleic Acids Res 1991 19 2539 2566 10.1093/nar/19.10.2539 2041731 (Pubitemid 21896888)
13. Regulation of expression of Eco29kI restriction-modification system. M Nagornykh, PhD thesis Institute of Biochemistry and Physiology of Microorganisms RAS. Molecular Biology department 2010
14. Construction of an overproducing strain, purification, and biochemical characterization of the 6His-Eco29kI restriction endonuclease. D Nikitin M Mokrishcheva M Denjmukhametov A Pertzev M Zakharova A Solonin, Protein Expr Purif 2003 30 26 31 10.1016/S1046-5928(03)00072-X 12821318 (Pubitemid 36815229)
15. 6His-Eco29kI methyltransferase methylation site and kinetic mechanism characterization. D Nikitin M Mokrishcheva A Solonin, Biochim Biophys. Acta 2007 1774 1014 1019 17604705 (Pubitemid 47189718)
16. Characterization of AloI, a Restriction-modification System of a New Type. E Cesnaviciene M Petrusiyte R Kazlauskiene Z Maneliene A Timinskas A Lubys A Janulaitis, J Mol Bio 2001 314 205 216 10.1006/jmbi.2001.5049 (Pubitemid 33105087)
17. Characterization of BcgI, a New Kind of Restriction-Modification System. H Kong S Roemer P Waite-Rees J Benner G Wilson D Nwankwo, J Biol Chem 1994 269 683 690 8276869 (Pubitemid 24026713)
18. Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 5'-CTCAG(N)(10/8)/. S Jurenaite-Urbanaviciene R Kazlauskiene V Urbelyte Z Maneliene M Petrusyte A Lubys A Janulaitis, Nucleic Acids Re 2001 29 895 903 10.1093/nar/29.4.895 (Pubitemid 32162257)
19. BseRI a novel restriction endonuclease from a Bacillus species which recognizes the sequence 5'.GAGGAG.3'. R Mushtaq S Naeem A Sohail S Riazuddin, Nucleic Acids Res 1993 21 3585 10.1093/nar/21.15.3585 8346041 (Pubitemid 23241505)
20. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. G Gemmen R Millin D Smith, Nucleic Acids Res 2006 34 2864 2877 10.1093/nar/gkl382 16723432 (Pubitemid 44540415)
21. Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11. K Lepikhov A Tchernov L Zheleznaja N Matvienko J Walter TA Trautner, Nucleic Acids Res 2001 29 4691 4698 10.1093/nar/29.22.4691 11713319 (Pubitemid 33095030)
22. Two novel restriction endonucleases from Campylobacter jejuni. J Vitor R Morgan, Gene 1995 157 109 110 10.1016/0378-1119(94)00668-I 7607469
23. Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco57I to select the mutant with a novel sequence specificity. R Rimseliene Z Maneliene A Lubys A Janulaitis, J Mol Biol 2003 327 383 391 10.1016/S0022-2836(03)00142-6 12628245 (Pubitemid 36298709)
24. The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide. A Piekarowicz M Golaszewska A Sunday M Siwiska D Stein, J Mol Biol 1999 293 1055 1065 10.1006/jmbi.1999.3198 10547285
25. Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes. J Nakonieczna T Kaczorowski A Obarska-Kosinska JM Bujnicki, Appl Environ Microbiol 2009 75 212 223 10.1128/AEM.01322-08 18997032
26. Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. S Jurenaite-Urbanaviciene J Serksnaite E Kriukiene J Giedriene C Venclovas A Lubys, PNAS 2007 104 10358 10363 10.1073/pnas.0610365104 17553965 (Pubitemid 47185670)
27. The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes. M Denjmukhametov M Brevnov M Zakharova A Repyk A Solonin O Petrauskene E Gromova, FEBS Lett 1998 433 233 236 10.1016/S0014-5793(98)00921-1 9744801 (Pubitemid 128369968)
28. Shaping the genome - restriction-modification systems as mobile genetic elements. I Kobayashi A Nobusato N Kobayashi-Takahashi I Uchiyama, Curr Opin Genet Dev 1999 9 649 656 10.1016/S0959-437X(99)00026-X 10607611
29. J Sambrook EF Fitsch T Maniatis, Molecular Cloning: A Laboratory Manual Cold Spring Harbor, Cold Spring Harbor Press 1989
30. Characterization of the genes coding for the Eco RV restriction and modification system of Escherichia coli. L Bougueleret M Schwarzstein A Tzugita M Zabeau, Nucleic Acids Res 1984 12 3659 3676 10.1093/nar/12.8.3659 6328432
31. Cloning type-II restriction and modification genes. K Lunnen J Barsomian R Camp C Card S Chen R Croft M Looney M Meda L Moran D Nwankwo, et al. Gene 1988 74 25 32 10.1016/0378-1119(88)90242-9 3074013 (Pubitemid 19069349)
32. Cloning and characterization of rec A gene from Pseudomonas aeruginosa. E Zaitzev E Zaitzeva I Bakhlamova V Gorelov N Kuzmin V Kryukov V Lanzov, Genetika (Russian) 1986 22 2721 2727 (Pubitemid 17209736)
33. Characterization of the ternary complex between Rab7, REP-1 and Rab geranylgeranyl transferase. K Alexandrov I Simon V Yurchenko A Iakovenko E Rostkova AJ Scheidig RS Goody, Eur J Biochem 1999 265 160 170 10.1046/j.1432-1327.1999.00699.x 10491170 (Pubitemid 29466024)
34. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. U Laemmli, Nature 1970 227 680 685 10.1038/227680a0 5432063
35. EcoRI methylase. Physical and catalytic properties of the homogeneous enzyme. R Rubin P Modrich, J Biol Chem 1977 252 7265 7272 332688 (Pubitemid 8205562)